proteins Flashcards
what is an amino acid
1) they are monomers of proteins
2) contain carbon, hydrogen, nitrogen and oxygen
3) they have an amine group, (r)-variable group and a carboxylic group
learn how to draw it - in booklet
how is a peptide bond made ?
when a condensation reaction occurs between two amino acids - the bond between the two amino acids
forms a dipeptide
what is a polypeptide ?
its a polymer of amino acids (3 or more)
which 2 groups condense to form a peptide bond ?
the carboxyl group from one amino acid (OH) and the amine group of another amino acid (H)
primary structure definition ?
the number and sequence of amino acids in a polypeptide chain
secondary structure definition ?
the way polypeptide chains fold into alpha helixes and/or beta pleated sheets
held together by weak hydrogen bonds only
what is the tertiary structure ?
*folding of polypeptide chain into specific complex 3D shape
*the r group determines how the polypeptide chain folds
1) weak hydrogen bonds
2) ionic bonds between oppositely charged R groups
3) disulphide bridges between cytosine amino acids only
quaternity structure
2 or more polypeptide chains
name 4 different proteins
1) enzyme - catalyse metabolic reactions
2) antibodies - bind to on specific antigens
3) structural proteins - provides strength and support
4) transport proteins - channel and carrier proteins
biurets test for protein
1) add NAOH to make sample alkaline
2) add a few drops of biurets solution
3) colour change from blue to purple means protein is present
function of enzyme
1) enzymes are proteins with specific tertiary structures
2) the active sights complimentary to one substrate
3) biological catalyst - speeds up reactions by lowering activation energy
4) can be intercellular or extracellular
5) determines structure and function of cells and whole organisms
lock and key model
- The active site is rigid and does not change shape
- The substrate enters/binds to the enzymes active site
- The substrate fits exactly into the active site – they are complementary
- Products are formed and no longer fit into the active site, so is released
- The enzyme is free to take part in another reaction
induced fit model
active sight is not complimentary
- The substrate enters the enzymes active site and binds to it Forming the ESC
- The binding of the substrate molecule/s induces the change in the shape of the active site.
- The ‘slight’ change in shape of the specific 3D tertiary structure of the active site, applies stress or distorts the bonds within the substrate(s) molecule(s) which lowers the Ea of the reaction.
- When substrate leaves, the active site returns to its original shape.
how does temp affect enzymes
Every enzyme has a specific temperature at which it works best (optimum). As the temperature increases up to its optimum the enzyme and substrate molecules increase their kinetic energy and are more likely to successfully collide and react. The rate of the reaction increases as the temperature increases because more Enzyme-Substrate complexes form per second
Optimum Temperature – The maximum energy that can be supplied to the molecules before hydrogen and ionic bonds start to break.
If the temperature is increased, beyond the optimum, then the atoms within the amino acid structure of the enzyme vibrate faster as they have more kinetic energy. This causes the weak Hydrogen bonds and ionic bonds between the R groups of neighbouring/adjacent amino acids to break, this causes a change in the specific tertiary structure, which may change the shape of the active site.
If the shape of the active site is changed, it will no longer be complementary to the enzymes substrate, meaning less/no more enzyme substrate complexes can be formed.
The enzyme is denatured (permanently changed 3D Tertiary structure of active site) and can no longer catalyse any chemical reactions.
effect of ph
pH is a measure of Hydrogen ion (H+) concentration. If the pH is changed from the optimum (more acidic or more basic) then the charge on the R groups of the amino acids are altered and ionic bonds (and weak H bonds) in the tertiary structure are broken.
The active site changes shape and the substrate can no longer fit (not specifically complementary). Less/No enzyme substrate complexes can be formed and the rate of the reaction decreases either side of the optimum. The enzyme is denatured.
IMPORTANT: Different enzymes will have different optimum pH’s depending on the role of the enzyme and where it is found in the body. E.g peptidases in the stomach work best at low pH (ACIDIC)
pH is recorded in a logarithmic scale, so a small change in the pH is actually a very large change in the number of H+ / protons.
Enzymes are very sensitive to pH change as just a slight change can result in charge differences at the active site preventing enzyme-substrate complexes forming. Binding of molecules is affected by charges on both molecules.
substrate concentration
Describe: As the substrate concentration increases, the rate of reaction increases and then levels off/plateaus at X.
Explain: When the substrate concentration is low the rate of reaction is low as there are less collisions and so few enzyme-substrate complexes form per second. The substrate is a limiting factor.
As the substrate concentration increases, more active sites are filled and the rate of reaction increases, due to more enzyme-substrate complexes forming. The substrate is a limiting factor.
competitive inhibitor
Competitive inhibitors have a similar structure to substrates.
They bind to the active site and prevent the substrate from binding temporarily.
Fewer enzyme substrate complexes form per second.
They reduce the rate of reaction so fewer products are formed per second (but SOME product will still be formed because some active sites can bind to a substrate)
It will take longer for all substrates to eventually form products (when compared to no inhibition).
- Inhibitor is a similar shape to substrate;
- Inhibitor binds to the active site ;
- Less substrate binds/fewer e-s complexes.
- So less (named product) is produced
non competitive inhibitor
Bind to a site on the enzyme which is away from the active site. This is known as an allosteric site.
When they bind to the enzyme it causes a conformational change to the shape of the active site so that substrate/s cannot bind. Binding can be temporary or permanent, however, if it detaches from one enzyme it is free to bind to another enzyme.
Fewer enzyme substrate complexes can be formed and the rate of reaction is decreased.
Fewer products are formed as a result. If all enzymes are inhibited then very few products will be produced overall.
It has the same effect as reducing the total number of enzymes.
Explain how a non-competitive inhibitor works
- Inhibitor is not a similar shape to substrate;
- Inhibitor binds away from active site /at allosteric site;
- Changes the shape of active site;
- Less substrate binds/fewer e-s complexes.
- Less (named product) formed
Explain how enzymes lower activation energy.
the enzyme puts strain on the substrate molecules, distorting the bonds in the substrate and lowering the activation energy required to break the bonds
What is a metabolic pathway?
sequence of enzymatically catalysed chemical reactions in a cell
